4C3O | pdb_00004c3o

Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella

• PDB DOI: https://doi.org/10.2210/pdb4C3O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 


• Deposited: 2013-08-26 Released: 2014-01-29 
• Deposition Author(s): Bowman, L., Flanagan, L., Fyfe, P.K., Parkin, A., Hunter, W.N., Sargent, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.205 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

How the Structure of the Large Subunit Controls Function in an Oxygen-Tolerant [Nife]-Hydrogenase.

Bowman, L., Flanagan, L., Fyfe, P.K., Parkin, A., Hunter, W.N., Sargent, F.

(2014) Biochem J 458: 449

• PubMed: 24428762 
• DOI: https://doi.org/10.1042/BJ20131520
• Primary Citation Related Structures: 
  4C3O


• PubMed Abstract: 
  

  Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure was determined to a resolution of 3.2 Å and the hydro-genase was observed to comprise associated large and small subunits. The structure indicated that His229 from the large subunit was close to the proximal [4Fe-3S] cluster in the small subunit. In addition, His229 was observed to lie close to a buried glutamic acid (Glu73), which is conserved in oxygen-tolerant hydrogenases. His229 and Glu73 of the Hyd-5 large subunit were found to be important in both hydrogen oxidation activity and the oxygen-tolerance mechanism. Substitution of His229 or Glu73 with alanine led to a loss in the ability of Hyd-5 to oxidize hydrogen in air. Furthermore, the H229A variant was found to have lost the overpotential requirement for activity that is always observed with oxygen-tolerant [NiFe]-hydrogenases. It is possible that His229 has a role in stabilizing the super-oxidized form of the proximal cluster in the presence of oxygen, and it is proposed that Glu73could play a supporting role in fine-tuning the chemistry of His229 to enable this function.

---

Organizational Affiliation: 
• *Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.
†Department of Chemistry, University of York, Heslington, York YO10 5DD, England, U.K.
‡Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 292.38 kDa 
• Atom Count: 20,051 
• Modeled Residue Count: 2,537 
• Deposited Residue Count: 2,592 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE-1 LARGE SUBUNIT	A, C, E	585	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  EC: 1.12.7.2 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for Q8ZPH0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPH0  Go to UniProtKB:  Q8ZPH0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE-1 SMALL SUBUNIT	B, D, F	279	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  EC: 1.12.7.2 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for Q8ZPG9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPG9  Go to UniProtKB:  Q8ZPG9

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	AA [auth F], M [auth B], S [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S	O [auth B], U [auth D], Z [auth F]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
F3S	BA [auth F], N [auth B], T [auth D]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFU	G [auth A], Q [auth C], V [auth E]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C3 H Fe N2 Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N
SO4	CA [auth F], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth A], I [auth A], J [auth A], K [auth A], W [auth E], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	L [auth A], R [auth C], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.205 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.46	α = 90
b = 122.21	β = 95.56
c = 227.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Bowman, L., Flanagan, L., Fyfe, P.K., Parkin, A., Hunter, W.N., Sargent, F.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Source and taxonomy
• Version 2.0: 2018-06-27
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary